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georgeg
Pjotr Prins 4 years ago
parent
commit
be14b238eb
  1. 3
      Makefile
  2. 10
      README.md

3
Makefile

@ -15,7 +15,7 @@ endif
DLIBS = $(LIBRARY_PATH)/libphobos2-ldc.a $(LIBRARY_PATH)/libdruntime-ldc.a
DLIBS_DEBUG = $(LIBRARY_PATH)/libphobos2-ldc-debug.a $(LIBRARY_PATH)/libdruntime-ldc-debug.a
SRC = $(wildcard bio/std/*.d) $(wildcard bio/std/*/*.d) bio.std.experimental.hts/bgzf.d bio/core/bgzf/constants.d
SRC = $(wildcard bio/std/*.d) $(wildcard bio/std/*/*.d) bio/std/experimental/hts/bgzf.d bio/core/bgzf/constants.d
OBJ = $(SRC:.d=.o)
BIN = bin/biod_tests
@ -42,3 +42,4 @@ check: $(BIN)
clean:
rm -vf $(OBJ)
rm -v $(BIN)
# find -name '*.o' -exec rm \{\} \;

10
README.md

@ -3,7 +3,7 @@
[BioD](https://github.com/biod/BioD) is a fast and memory efficient bioinformatics library written in the [D programming language](http://www.dlang.org)
whose aim is to:
* Provide a platform for developing high-performance computational biology applications using the [D programming language](http://www.dlang.org) through
* Provide a platform for developing high-performance computational biology applications using the [D programming language](http://www.dlang.org) through
- Automatic parallelization of tasks where possible
- Avoiding unnecessary memory allocations
@ -15,13 +15,13 @@ hybrid object orientated and functional (OOP/FP) programming language with templ
than that of C++.
## D programming language resources
* [The D Programming Language](https://www.amazon.com/D-Programming-Language-Andrei-Alexandrescu/dp/0321635361) by Andrei Alexandrecu
* [The D Programming Language](https://www.amazon.com/D-Programming-Language-Andrei-Alexandrescu/dp/0321635361) by Andrei Alexandrecu
* [Programming in D](http://ddili.org/ders/d.en/index.html) by Ali Çehreli.
* [The D Cookbook](https://www.amazon.com/D-Cookbook-Adam-D-Ruppe/dp/1783287217) by Adam D. Ruppe
* [The D Cookbook](https://www.amazon.com/D-Cookbook-Adam-D-Ruppe/dp/1783287217) by Adam D. Ruppe
## Current development
Our aim is to provide several modules to work with biological datasets.
BioD provides modules for manipulating high throughput data formats by provifing fast and easy to use native BAM file reader and writer
BioD provides modules for manipulating high throughput data formats by provifing fast and easy to use native BAM file reader and writer
with ability to Iterate a BAM file a read at a time,a nucleotide at a time (pileup) or via a sliding window.
@ -35,7 +35,7 @@ The current default is to provide the path to the checked out repo to the D-comp
It is possible to create a recent build container with GNU guix
`guix enviroment -C guix --ad-hoc meson ninja ldc dub zlib gdb --network`
`guix environment -C guix --ad-hoc meson ninja ldc dub zlib gdb --network`
and run meson and ninja (see the meson branch of BioD)

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